Not just Underwater Ruins or an Underwater Base, but an entire city of people living and "breathing" underwater. It's usually created with futuristic technology or powerful magic, and a popular depiction is to have a fully surviving Atlantis with domes and/or water breathing Fish People or Apparently Human Merfolk. Usually though it's a modern attempt at colonizing the ocean floor, or a villain's secret lair.

As might be expected, living in such a precarious location makes these cities inordinately prone to having something go Horribly Wrong. Be it sabotage causing the dome to break, an undersea volcano activating, or other disasters.

Examples:

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Anime & Manga

Daphne in the Brilliant Blue: The main cities of the aquaticNew Eden were originally Underwater Cities created to escape the apocalypse. Heroine Maia is the last survivor of one of the cities which was destroyed before it could surface.

The Fishman Island in One Piece is actually a big mass of land floating in a 2-layer resin bubble, underwater. The light source come from the mystical Sunlight Tree Eve, which transfers sunlight from the surface to the ocean deep.

PokÚdex: The Jellicent are the keepers of one beneath a massive, Jellicent-shaped dome, made out of shipwrecks and flotsam, lit and warmed by underwater vents and populated by sailors kidnapped en masse when their ships pass through the Jellicent's territory. The purpose for this seems to be so that the Jellicent can have access to human technology.

Film — Animated

The Little Mermaid: Atlantica, and underwater city or kingdom inhabited by mermaids and talking sea life.

My Little Pony: The Movie (2017) has an underwater city at Mt Aris. The hippogriffs fled the Storm King's forces and transformed themselves into seaponies to hide there.

Film — Live-Action

City Beneath The Sea a Made-for-TV Movie from the 70s about two futuristic divers discovering an underwater city that must be protected from alien forces. It was intended as a pilot for a TV series (produced by Irwin Allen) but never got picked up.

The City Under The Sea (1965), AKA War Gods of the Deep, a B-movie from the 60s features a Mad Scientist keeping a girl hostage in a city full of advanced humans with extended lifespans.

The Underwater City (1962) details a group of people testing out experimental underwater housing - and disaster strikes when the settlement caves in.

Otoh Gunga, home of the Gungans from the Star Wars prequels, made out of a large number of sealed-off, interconnected domes at the bottom of a large lake.

The Abyss, in which the NTIs have a very large habitat on the ocean floor. (Whether it's a city or an enormous starship is never really made clear.)

Handled as realistically as possible in "Ocean on Top" by Hal Clement. A colony of humans is established on the ocean floor, using geothermal power to provide light and a specially-made oxygen-carrying dive fluid in place of air. But since the humans are less dense than water, the humans have to wear weights if they want to stay on the bottom or even have neutral buoyancy. They sleep tied to the ceilings of their buildings.

Somewhereinitaly in Almost Night. There was also a city called Somewherenotinitaly, but it was destroyed by the Deep Ones.

Animorphs has an odd book where the heroes, plus Visser Three, get trapped in a city in an underwater cave. The inhabitants are amphibious mutants whose race is dying, which means that they harvest any humans who sink for DNA.

They also visit the City of Worms (it's nicer than it sounds) on Leera, an ocean world inhabited by frog-like aliens.

In Everworld, Poseidon and Neptune both have underwater cities, and they're fighting over Atlantis. We mostly see Neptune's city, where water can be drained, or humans made amphibious, based on the god's whim. (This is not encouraging.)

In Underneath A Merfolk Tale the merfolk population lives in The City. The merfolk in the story actually live in land and have little dealings with it, although their history and their reasons for leaving it are part of the plot.

In the first episode, the city is discovered to be underwater, having been submerged by the Ancients to escape constant orbital bombardment from the Wraith. In a subversion of the Gone Horribly Wrong situation mentioned above, when the shield fails, the city surfaces.

In a Double Subversion, It didn't happen the first time around: In an alternate timeline, the city was flooded, and Dr. Weir escaped drowning in a time-traveling ship; she then convinced Ancient scientist Janus to add the fail-safe.

seaQuest DSV is set in a world where the ocean floor has been so heavily colonized that there are whole underwater nations.

In the cartoon segments of The Aquabats! Super Show!, the band tries infiltrate an underwater city beneath the moon's surface to save Jimmy the Robot.

In Star Trek: The Next Generation, still reeling from his recent assimilation by the Borg, Picard is briefly tempted in "Family" to quit Starfleet and join the Atlantis Project, who are aiming to build one of these on the floor of the Atlantic Ocean.

Jonas Brothers sung of this, where as a product of a time machine, everyone lives underwater;

"I've been to the year 3000.

Not much has changed but they lived under water."

Tabletop Games

Several Dungeons & Dragons settings include undersea civilizations of merfolk, tritons, sahuagin or the like; some of these use air-filled domes as housing for surface-dwelling visitors. The Known World/Mystara campaign setting has the Kingdom of Aquas, which was once part of the Empire of Alphatia.

In New Horizon, Aquilon's Reach has multiple underwater cities, as well as some atop glaciers. Unsurprisingly, they also boast the best navy in game.

Shadowrun: In the 2nd Edition supplement Portfolio of a Dragon: Dunkelzhan's Secrets, the last will of the titular dragon left a bequest of five million nuyen to the first party to establish a self-sustaining community of at least 100 persons on the ocean floor. Yamatetsu Corporation eventually won the bequest with their SoaTome AquaDomes.

Transhuman Space has Elandra, an Australian-founded "free city" under the Pacific. It's more of a town than a city, really, but a respectably-sized one.

Numenera: Several exist, some in fairly shallow parts of the sea and some in the blackest depths. Their inhabitants collectively refer to these places as oceia.

Joria is a city built on the back of an enormous crustacean called a granthu, which moves in a roughly constant orbit around the ocean floor. The city is partly open to water, and inhabited by a species of amphibious humanoids called Jorians. The Jorians believe that there are other cities of their kind on the backs of other granthus, following their own orbits somewhere in the global ocean, and put in a great deal of time and effort in searching for them.

The City of Rust is a large settlement on top of a massive slab resting on the ocean floor, which gets its name from the rust-red metal making up its buildings. It's mostly inhabited by a species of aquatic aliens called the skeane, and watched over by four massive and fickle AIs that its inhabitants worship as gods.

Ahmas is a city in the darkest depths of the ocean, home to the descendants of humans who were transformed into monstrous Fish People by mysterious entities centuries in the past.

Morenel is a city on the abyssal plain inexplicably inhabited by humans, who have been living there longer than any surface-based human civilization has been around.

Onisteles is a colossal sea sponge that was colonized by an aquatic race called the glanae. The skin flakes the glanae shed feed the sponge, which in turn provides them with a home in a symbiotic relationship. What the glanae don't know is that Onisteles is in a similar relationship with a species of predatory animals called the ebons, where the predators protect the city from certain sponge-eating slugs... in exchange for Onisteles occasionally spitting out glanae to feed the ebons.

In the 20th Anniversary edition of Mage: The Awakening, the Avatar Storm cut off the Technocratic Union from bases maintained in Horizon Realms. In order to have bases of operation relatively secure from the prying eyes of the Sleepers as well as the Traditions, several of the Underwater Bases previously maintained solely by the Void Engineers have been converted (or are in the process of conversion) into full-on cities with representatives from all of the Union's Conventions.

Video Games

Rapture from BioShock is a Diesel Punk and Bio Punk city that's completely underwater, save for a lighthouse that contains a bathysphere to bring people down from the surface.

Aquaria has Mithalas City, which has long since been completely ruined after a Path of Inspiration corrupted its patron deity into a horrible monster. Guess what you end up fighting in the ruined cathedral.

In Mass Effect, it's mentioned that Kahje, the homeworld of the aquatic hanar has 90% of the surface covered by water and features impressive domed cities, which they originally built for the drell after the hanar rescued most of the species from their dying homeworld, two centuries previously.

ANNO 2070 has underwater cities...except they aren't actually cities. Rather, they're underwater plateaus (implied in-game to be parts of our world submerged by climate change) which all three major factions can build farms and factories on. These largely-automated facilities provide supplies which are rare or nonexistent abovewater, making them a key part of the middle and late-game. The game's lesser faction, the S.A.A.T. (Scientific Academy for Advanced Technologies) specialises in building and working with such settlements, an attribute which was further developed in the game's expansion, The Deep Sea.

Sunless Sea: There are several populated cities beneath the Unterzee that you can visit once you get the Zubmariner expansion. Most have their own unique peculiarities — Hideaway is built on the shell of a colossal hermit crab, Dahut is populated by Drownies and has water that can be breathed like air, Wrack is built out of sunken ships and home to wreckers, Nook is tucked into the maw of... something huge and lamprey-like, and Anthe is built into a crystal formation and home to people who seek to become more crystalline themselves.

Zukahnaut's protagonist finds himself first imprisoned in, then ruling over, an undersea kingdom in a story where he swaps bodies with its leader.

In Girl Genius, London is a domed city, after a cabal of Sparks caused the whole of Great Britain to start sinking for reasons unknown. The state of other cities is so far unrevealed.

Web Original

In The Gamer's Alliance, Adlivun is a thriving underwater city populated by merfolk known as merrows.

Western Animation

Futurama featured the Lost City of Atlanta — a joke on Atlantis, of course — which was turned into a City on the Water to attract more tourism, but became overloaded with buildings and construction and sank. The citizens who stayed behind ended up evolving into mermaids and mermen by the 3000's, thanks to the caffeine from the Coca-Cola plant (somehow) speeding up their evolution.

This is the year two thousand and twenty. The place is the Challenger seamount, the top of an underwater mountain, a complex beneath the sea. 250 men, women and children live here, each of them a scientist-pioneer. For this is our last frontier, a hostile environment which may hold the key to tomorrow. Each day these oceanauts meet new challenges, as they build their city beneath the sea. This is Sealab 2020.

King had Bubble Town, the capital of the nation of Undersea, ruled over by the despotic Cousin Tess.

The Adventures of Super Mario Bros. 3 had one in the episode "The Ugly Mermaid". It was a bizarre case in that the city had domes with air in them, despite the merfolks not being able to breathe air.

Samurai Jack: The episode "Jack Under the Sea" features the underwater city of Oceanus, home of an amphibious alien tribe called the Triseraquins, built as a system of waterproof domes on top of high-tech towers. It used to be a City on the Water instead, but Aku banished it beneath the ocean to where it is now. It returns to the surface by the end of the episode.

The Little Mermaid in addition to Atlantica, also features the Eel-Ectric City - a metropolis that's "so hopping it's always bopping".

Real Life

The Philippines used to be this before it was settled by animals and later, humans.

Community

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